The movie follows former dolphin trainer Ric O'Barry's quest to document the dolphin hunting operations in Taiji, Wakayama, Japan. In the 1960s, O'Barry captured and trained the five wild dolphins who would play the role of "Flipper" in the hit television series of the same name. This pop-culture phenomenon fueled widespread public adoration of dolphins. It was when one of the dolphins committed a form of suicide in his arms, closing her blowhole voluntarily in order to suffocate, that O'Barry came to see it as a curse not a blessing. Days later, he found himself being arrested off the island of Bimini, attempting to cut a hole in the sea pen in order to set free a captured dolphin. Since then O'Barry has worked tirelessly as an advocate on behalf of dolphins around the world.[clarification needed]
After meeting with O'Barry, Psihoyos and his crew travel to the small town of Taiji, a town that appears to be devoted to the wonder of the dolphins and whales that swim off their coast. But in an isolated cove, surrounded by wire and "Keep Out" signs, some of the townspeople hide a stark reality. It is here that the fishermen of Taiji, driven by a multi-billion dollar dolphin entertainment industry and a dubious and artificial market for mercury-tainted dolphin meat, engage in the unseen killing. Local volunteers physically block attempts by outsiders to view the dolphin killing taking place in the cove. Together with the Oceanic Preservation Society, Psihoyos, O'Barry, and the crew utilize special tactics and embark on a mission to get the truth on what is really going on in the cove and why it matters to everyone else in the world.